History¶
18.9.2.dev0¶
18.9.1 (2018-09-15)¶
- More work improving channel handling for mulled containers.
18.9.0 (2018-09-14)¶
- Update Conda channel order (thanks to @bgruening).
- Bring in the latest Galaxy changes and add Galaxy XSD to the project.
- Various cwltool fixes (thanks to @nsoranzo).
18.5.15 (2018-09-12)¶
- More tweaks to CWL tool loading to support newer versions of cwltool.
18.5.14 (2018-09-12)¶
- Improved tool linting and reporting thanks to @natefoo and @nsoranzo.
- Add support for newer cwltool thanks to @nsoranzo.
- Improved mulled building thanks to @pcm32.
18.5.13 (2018-05-23)¶
- Small updates to test parsing to support Galaxy workflow testing.
18.5.12 (2018-05-22)¶
- Update test data processing to allow URIs in Galaxy workflow tests.
18.5.11 (2018-05-16)¶
- Parse CWL SoftwareRequirements to Galaxy requirements (required to fix various Planemo functionality for CWL tools).
18.5.10 (2018-05-10)¶
- Docker logging API fix for Planemo.
18.5.9 (2018-05-07)¶
- Update CWL linting to target CWL 1.0.
18.5.8 (2018-05-06)¶
- Better error handling for Conda searching (thanks to @bgruening).
- Update against the latest Galaxy codebase.
- Add Galaxy tool linting to ensure versions are PEP 440 compliant (thanks to @davebx).
18.5.7 (2018-03-12)¶
- More tool testing client fixes, this time for ephemeris.
18.5.6 (2018-03-12)¶
- Bring in the latest Galaxy dev branch - includes code cleanup and many Python 3 fixes from @nsoranzo as well as client code for executing tool tests against external Galaxy instances.
- Extend tool testing client from Galaxy’s dev branch with even more data collection for compatiblity with Planemo.
18.5.5 (2018-03-06)¶
- Fix mulled to use shlex.quote to escape single quotes in test command (thanks to @mbargull).
- Make markupsafe a dependency since it is import unconditionally in galaxy.tools.toolbox (thanks to @mbargull).
- Python 3 fix for assertion testing.
18.5.4 (2018-03-01)¶
- Make conda image for mulled builds configurable via an environment variable (thanks to @mbargull).
18.5.3 (2018-02-28)¶
- Fix path module for import on Windows for Pulsar.
18.5.2 (2018-02-28)¶
- Various fixes for library usage mostly related to Conda (with help from @nsoranzo).
18.5.1 (2018-02-26)¶
- Redo last release - pushed to PyPI without actually including the desired fix.
18.5.0 (2018-02-26)¶
- Another Python 3 fix for Planemo.
- Fix galaxy-lib version - this has actually been tracking the 18.05 release of Galaxy for the last two releases.
18.1.0 (2018-02-26)¶
- More Python 3 fixes for Planemo thanks to @nsoranzo.
- Bring in the latest Galaxy development branch.
17.9.12 (2018-02-22)¶
- Python 3 fix for Planemo thanks to @nsoranzo.
- Fix bad merge of miniconda update for mulled work.
17.9.11 (2018-02-22)¶
- Update to the latest Galaxy dev just prior to the branch of 18.01.
- Python 3 fixes.
17.9.10 (2017-11-23)¶
- Added docs for using mulled-build with your own quay.io account (thanks to @jerowe).
- Catch errors in Conda search if nothing is found (preventing planemo-monitor from functioning properly) (thanks to @bgruening).
- Make multi-requirement container building via mulled more stable (thanks to @bgruening).
17.9.9 (2017-09-27)¶
- Bring in latest updates from the 17.09 branch of Galaxy - including updating the default target Conda version and fixes for module resolution.
17.9.8 (2017-09-26)¶
- Bring in updated CWL utilities from the upstream work on CWL integration.
17.9.7 (2017-09-19)¶
- Bring in updated CWL utilities from the upstream work on CWL integration.
17.9.6 (2017-09-15)¶
- Remove
command
lint check that is no longer valid.
17.9.5 (2017-09-06)¶
- Bring in updated CWL utilities from the upstream work on CWL integration.
17.9.4 (2017-09-06)¶
- Bring in various Galaxy updates including numerous Conda fixes and changes (thanks to @nsoranzo).
- Improved error handling when parsing tool reStructuredText (thanks to @erasche).
- Updated CWL utilities.
17.9.3 (2017-06-27)¶
- Bug fix in from_dict parsing of tool dependency specs.
17.9.2 (2017-06-22)¶
- Sync with mulled enhancements and fixes from Galaxy’s development branch.
17.9.1 (2017-06-17)¶
- Various small Singularity fixes and enhancements.
17.9.0 (2017-06-11)¶
- Bring in latest Galaxy dev changes.
- Implement support for building Singularity mulled containers.
- Implement mulled version 2 package hashing.
- Fix default namespace for mulled operations from mulled to biocontainers.
17.5.11 (2017-05-31)¶
- Fix HISTORY.rst formatting to properly render release on PyPI.
- Fix bug in new offline Conda search function introduced in 17.5.10.
17.5.10 (2017-05-30)¶
- Always clean up build directory in mulled commands (thanks to @johanneskoester).
- Expose offline mode in Conda search utility (for repeated fast searches).
- When publishing mulled containers - use quay.io API to publish them as public.
- Add explicit option
--check-published
tomulled-build-*
. - Fix auto-installation of Involucro on first attempt.
- Handle explicit tags in
mulled-build-files
and add an implicit tag of0
if none found. - Fix tab parsing in
mulled-build-files
.
17.5.9 (2017-05-16)¶
- Make mulled-search to search biocontainers instead of mulled repository by default (thanks to @tom-tan).
- Allow setting a new base image with mulled-build.
17.5.8 (2017-04-23)¶
- Fix mulled image cleanup. #55.
17.5.7 (2017-03-15)¶
- Updates to CWL library functionality for several months worth of CWL tool updates.
- Allow finding tools by a URI-like strings (e.g.
file://
,http://
,dockstore://
). - Bring in latest Galaxy updates.
17.5.6 (2017-03-01)¶
- Expanded options for mulled CLI tools and library functionality. Fixes #49.
17.5.5 (2017-02-26)¶
- Fix bug in 17.5.4 where under certain conditions conda-build would attempt to be setup with the conda –use-local flag - which is not allowed.
17.5.4 (2017-02-26)¶
- Fix local builds Conda support to reflect conda-build is required.
- Fix default target path for miniconda installs.
17.5.3 (2017-02-24)¶
- Update against the latest Galaxy dev branch changes.
- Update Conda utilities to allow using locally built packages.
17.5.2 (2017-02-21)¶
- Conda utility enhancements to fix a Planemo bug.
17.5.1 (2017-02-21)¶
- Various improvements to Galaxy tool linting.
17.5.0 (2017-02-16)¶
- Bring in the last of the Galaxy dev changes.
- Allow Conda installs to target global Conda config (for Planemo)
17.1.2 (2017-01-23)¶
- Bring in the last of the Galaxy dev changes before branch of release_17.01.
- Improvements to mulled testing thanks to @mvdbeek.
17.1.1 (2016-12-14)¶
- Revert changes to shell command execution in Galaxy that had unintended consequences for Planemo.
17.1.0 (2016-12-12)¶
- Improved mulled logging thanks to @bgruening.
- Bring in the latest Galaxy dev changes.
16.10.10 (2016-10-24)¶
- Fix mulled package data fetching for Mac OS X (thanks to @dannon).
16.10.9 (2016-10-21)¶
- Small fixes including to reflect mulled name on quay.io changed to biocontainers.
16.10.8 (2016-10-10)¶
- More mulled enhancements and bug fixes thanks to @bgruening and @daler.
16.10.7 (2016-10-08)¶
- More mulled enhancements and bug fixes thanks to @bgruening.
- Fix bioconda support by adding conda-forge to list of default channels.
16.10.6 (2016-10-07)¶
- More mulled enhancements thanks to @bgruening.
16.10.5 (2016-10-04)¶
- Some docstring cleanup and minor tweaks to Conda support for downstream planemo mulled work.
16.10.4 (2016-10-03)¶
- More mulled fixes and enhancements.
16.10.3 (2016-10-02)¶
- Small mulled and Conda related fix and enhancements.
16.10.2 (2016-09-30)¶
- Fix setup.py for features in 16.10.1.
16.10.1 (2016-09-29)¶
- Updates for recents changes to Galaxy and initial mulled scripts and container resolver.
16.10.0 (2016-08-31)¶
- Updates for recent changes to Galaxy.
16.7.10 (2016-08-04)¶
- Updates for recent change to Galaxy.
16.7.9 (2016-06-13)¶
- Updates for recent changes to Galaxy and cwltool.
16.7.8 (2016-06-05)¶
- Updates to include Galaxy library for verifying test outputs and the latest dev changes to Galaxy.
16.7.7 (2016-05-23)¶
- Fixes to CWL and Docker libraries for Planemo.
16.7.6 (2016-05-11)¶
- Fixes to cwl processing for Planemo.
16.7.5 (2016-05-11)¶
- Updates to cwl processing for Planemo.
16.7.4 (2016-05-10)¶
- Updates to cwl processing for Planemo.
16.7.3 (2016-05-07)¶
- Updates to cwltool_deps for Planemo.
16.7.2 (2016-05-06)¶
- Updates to tool parsing and linting for Planemo.
16.7.1 (2016-05-02)¶
- Update against the latest development branch of Galaxy.
16.7.0 (2016-04-21)¶
- Update against the latest development branch of Galaxy.
16.4.1 (2016-04-08)¶
- Update against the latest development branch of Galaxy.
16.4.0 (2016-02-15)¶
- Update against the latest development branch of Galaxy.
16.1.9 (2016-01-14)¶
- Fix a bug in the source distribution of galaxy-lib.
16.1.8 (2016-01-12)¶
- Update against Galaxy’s release_16.01 branch.
16.1.7 (2016-01-03)¶
- Update against Galaxy’s dev branch - including conda updates, dependency resolution changes, and toolbox updates.
16.1.6 (2015-12-28)¶
- Additional fixes to setup.py and updates for recent changes to Galaxy’s dev branch.
16.1.5 (2015-12-22)¶
- Fix another bug that was preventing dependency resolution from working in Pulsar.
16.1.4 (2015-12-22)¶
- Another setup.py fix for job metrics module.
16.1.3 (2015-12-22)¶
- Python 3 fixes and updates for recent Galaxy dev commits.
16.1.2 (2015-12-21)¶
- Fix for missing galaxy.tools.parser package in setup.py.
- Fix LICENSE in repository.
16.1.1 (2015-12-20)¶
- Fix small issues with dependencies, naming, and versioning with first release.
16.1.0 (2015-12-20)¶
- Setup project.